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---
license: cc0-1.0
configs:
- config_name: default
data_files:
- split: train
path: data/train-*
- split: validation
path: data/validation-*
- split: test
path: data/test-*
dataset_info:
features:
- name: sequence
dtype: string
- name: modified_sequence
dtype: string
- name: precursor_mz
dtype: float64
- name: precursor_charge
dtype: int64
- name: mz_array
sequence: float64
- name: intensity_array
sequence: float32
splits:
- name: train
num_bytes: 839098224
num_examples: 499402
- name: validation
num_bytes: 49792990
num_examples: 28572
- name: test
num_bytes: 45505134
num_examples: 27142
download_size: 1119691599
dataset_size: 934396348
---
# Dataset Card for Nine-Species excluding Yeast
Dataset used for the baseline comparison of InstaNovo to other models.
## Dataset Description
- **Repository:** [InstaNovo](https://github.com/instadeepai/InstaNovo)
- **Paper:** [De novo peptide sequencing with InstaNovo: Accurate, database-free peptide identification for large scale proteomics experiments](https://www.biorxiv.org/content/10.1101/2023.08.30.555055v1)
### Dataset Summary
Dataset used in the original [DeepNovo](https://www.pnas.org/doi/full/10.1073/pnas.1705691114) paper.
- The training set contains 8 species excluding yeast
- The validation/test set contains the yeast species
## Dataset Structure
The dataset is tabular, where each row corresponds to a labelled MS2 spectra.
- `sequence (string)` \
The target peptide sequence excluding post-translational modifications
- `modified_sequence (string)` \
The target peptide sequence including post-translational modifications
- `precursor_mz (float64)` \
The mass-to-charge of the precursor (from MS1)
- `charge (int64)` \
The charge of the precursor (from MS1)
- `mz_array (list[float64])` \
The mass-to-charge values of the MS2 spectrum
- `mz_array (list[float32])` \
The intensity values of the MS2 spectrum
## Citation Information
If you use this dataset, please cite the original authors.
The original data is available on [MASSIVE](https://massive.ucsd.edu/ProteoSAFe/static/massive.jsp) with the identifier `MSV000081382`.
Please also cite InstaNovo:
```bibtex
@article{eloff_kalogeropoulos_2023_instanovo,
title = {De novo peptide sequencing with InstaNovo: Accurate, database-free peptide identification for large scale proteomics experiments},
author = {Kevin Eloff and Konstantinos Kalogeropoulos and Oliver Morell and Amandla Mabona and Jakob Berg Jespersen and Wesley Williams and Sam van Beljouw and Marcin Skwark and Andreas Hougaard Laustsen and Stan J. J. Brouns and Anne Ljungars and Erwin Marten Schoof and Jeroen Van Goey and Ulrich auf dem Keller and Karim Beguir and Nicolas Lopez Carranza and Timothy Patrick Jenkins},
year = {2023},
doi = {10.1101/2023.08.30.555055},
publisher = {Cold Spring Harbor Laboratory},
URL = {https://www.biorxiv.org/content/10.1101/2023.08.30.555055v1},
journal = {bioRxiv}
}
``` |